Jupyter Bridge and RCy3

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Installation

if(!"RCy3" %in% installed.packages()){
    install.packages("BiocManager")
    BiocManager::install("RCy3")
}
library(RCy3)

Required software

RCy3 works by connecting with Cytoscape. You will need to install and launch Cytoscape:

• Download the latest Cytoscape from http://www.cytoscape.org/download.php
• Complete installation wizard
• Launch Cytoscape

Jupyter Bridge

Jupyter-Bridge is a Flask service that executes on a server accessible to both a remote Jupyter server and browser-based Jupyter client. Code running on the server calls Jupyter-Bridge to queue a request that the client will execute, and the client will use Jupyter-Bridge to return a reply. This enables a workflow running on remote Jupyter to execute functions on a PC-local Cytoscape – the remote Jupyter runs the request through Jupyter-Bridge, where it is picked up by Javascript code running on the Jupyter web page in the PC-local browser, which in turn calls Cytoscape. The Cytoscape response travels the reverse route.

Jupyter-Bridge allows a remote Jupyter Notebook to communicate with a workstation-based Cytoscape as if the Notebook were running on the Cytoscape workstation. A Jupyter Notebook passes a Cytoscape call to an independent Jupyter-Bridge server where it’s picked up by the Jupyter-Bridge browser component and is passed to Cytoscape. The Cytoscape response is returned via the opposite flow. As a result, workflows can reside in the cloud, access cloud resources, and yet still leverage Cytoscape features.

Connect to local Cytoscape remotely

browserClientJs <- getBrowserClientJs()
IRdisplay::display_javascript(browserClientJs)

Check connection

cytoscapeVersionInfo()
cytoscapePing()

Execute Differentially Expressed Genes Network remotely

Visit the Jupyter Bridge and Differentially Expressed Genes Network Analysis for more information.